1E72 | pdb_00001e72

Myrosinase from Sinapis alba with bound gluco-hydroximolactam and sulfate or ascorbate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E4M	PDB ENTRY 1E4M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3 PRECIPITANT 66 % SAT. AMMONIUM SULFATE, 100MM TRIS-HCL PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.2	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.3	α = 90
b = 137.2	β = 90
c = 80.6	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	BENT MULTILAYER, SAGITALLY FOCUSING CRYSTAL	1998-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	37.3	99.7	0.076	0.076	5.2	4.2		110239

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	99.7		0.256	0.256	2	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1E4M	1.6	10	95835	4890	97.5	0.129	0.14	0.157	0.17	RANDOM	20.5

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	26.3
p_staggered_tor	11.7
p_planar_tor	8.2
p_scangle_it	3.8
p_mcangle_it	2.9
p_scbond_it	2.9
p_mcbond_it	2.2
p_multtor_nbd	0.305
p_singtor_nbd	0.17
p_xyhbond_nbd	0.161
p_chiral_restr	0.126
p_planar_d	0.043
p_angle_d	0.032
p_plane_restr	0.027
p_bond_d	0.019
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4016
Nucleic Acid Atoms
Solvent Atoms	787
Heterogen Atoms	329

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling